Fifty Years of IOCV, 1957 to 2007: From Graft-Transmitted Citrus Agents to Viroids, Viruses and Endogenous Bacteria

In November, 1957, the well-known Citrus Experiment Station (CES) of the University of California at Riverside, USA, celebrated its 50th anniversary. This was a good opportunity to hold the first international conference on so-called “virus” diseases of citrus, of which many had been studied in California, if not in Florida. Maladies such as Tristeza, Psorosis, Concave Gum and Blind Pocket, Crinkly leaf and Infectious variegation, Stubborn, Xyloporosis and Cachexia, Exocortis, and Vein enation had been shown to be transmissible by graft-inoculation. and were, for this reason, thought to be of viral nature, but not a single causal agent had yet been identified, mechanically transmitted, purified, or even seen in the electron microscop

ICTV Virus Taxonomy Profile: Ophioviridae

[EN] The Ophioviridae is a family of filamentous plant viruses, with single-stranded negative, and possibly ambisense, RNA genomes of 11.3-12.5 kb divided into 3-4 segments, each encapsidated separately. Virions are naked filamentous nucleocapsids, forming kinked circles of at least two different contour lengths. The sole genus, Ophiovirus, includes seven species. Four ophioviruses are soil-transmitted and their natural hosts include trees, shrubs, vegetables and bulbous or corm-forming ornamentals, both monocots and dicots. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the taxonomy of the Ophioviridae, which is available at http://www.ictv.global/report/ophioviridae.Production of this summary, the online chapter and associated resources was funded by a grant from the Wellcome Trust (WT108418AIA).Garcia, M.; Dal Bo, E.; Da Graca, JV.; Gago Zachert, SP.; Hammond, J.; Moreno, P.; Natsuaki, T.... (2017). ICTV Virus Taxonomy Profile: Ophioviridae. Journal of General Virology. 98(6):1161-1162. doi:10.1099/jgv.0.000836S1161116298

Towards an integrated computational method to determine internal spaces for optimum environmental conditions

Computational Fluid Dynamics tools and Response Surface Methodology optimization techniques were coupled for the evaluation of an optimum window opening design that improves the ventilation efficiency in a naturally-ventilated building. The multi-variable optimization problem was based on Design of Experiments analysis and the Central Composite Design method for the sampling process and estimation of quadratic models for the response variables. The Screening optimization method was used for the generation of the optimal design solution. The generated results indicated a good performance of the estimated response surface revealing the strength correlations between the parameters. Window width was found to have greater impact on the flow rate values with correlation coefficient of 73.62%, in comparison to the standard deviation 55.68%, where the window height prevails with correlation coefficient of 96.94% and 12.35% for the flow rate. The CFD results were validated against wind tunnel experiments and the optimization solution was verified with simulation runs, proving the accuracy of the methodology followed, which is applicable to numerous environmental design problems

Conservation of Gene Order and Content in the Circular Chromosomes of ‘Candidatus Liberibacter asiaticus’ and Other Rhizobiales

‘Ca. Liberibacter asiaticus,’ an insect-vectored, obligate intracellular bacterium associated with citrus-greening disease, also called “HLB," is a member of the Rhizobiales along with nitrogen-fixing microsymbionts Sinorhizobium meliloti and Bradyrhizobium japonicum, plant pathogen Agrobacterium tumefaciens and facultative intracellular mammalian pathogen Bartonella henselae. Comparative analyses of their circular chromosomes identified 514 orthologous genes shared among all five species. Shared among all five species are 50 identical blocks of microsyntenous orthologous genes (MOGs), containing a total of 283 genes. While retaining highly conserved genomic blocks of microsynteny, divergent evolution, horizontal gene transfer and niche specialization have disrupted macrosynteny among the five circular chromosomes compared. Highly conserved microsyntenous gene clusters help define the Rhizobiales, an order previously defined by 16S RNA gene similarity and herein represented by the three families: Bartonellaceae, Bradyrhizobiaceae and Rhizobiaceae. Genes without orthologs in the other four species help define individual species. The circular chromosomes of each of the five Rhizobiales species examined had genes lacking orthologs in the other four species. For example, 63 proteins are encoded by genes of ‘Ca. Liberibacter asiaticus’ not shared with other members of the Rhizobiales. Of these 63 proteins, 17 have predicted functions related to DNA replication or RNA transcription, and some of these may have roles related to low genomic GC content. An additional 17 proteins have predicted functions relevant to cellular processes, particularly modifications of the cell surface. Seventeen unshared proteins have specific metabolic functions including a pathway to synthesize cholesterol encoded by a seven-gene operon. The remaining 12 proteins encoded by ‘Ca. Liberibacter asiaticus’ genes not shared with other Rhizobiales are of bacteriophage origin. ‘Ca. Liberibacter asiaticus’ shares 11 genes with only Sinorhizobium meliloti and 12 genes are shared with only Bartonella henselae

Comparison of the ‘Ca. Liberibacter asiaticus’ Genome Adapted for an Intracellular Lifestyle with Other Members of the Rhizobiales

An intracellular plant pathogen ‘Candidatus Liberibacter asiaticus,’ a member of the Rhizobiales, is related to Sinorhizobium meliloti, Bradyrhizobium japonicum, nitrogen fixing endosymbionts, Agrobacterium tumefaciens, a plant pathogen, and Bartonella henselae, an intracellular mammalian pathogen. Whole chromosome comparisons identified at least 50 clusters of conserved orthologous genes found on the chromosomes of all five metabolically diverse species. The intracellular pathogens ‘Ca. Liberibacter asiaticus’ and Bartonella henselae have genomes drastically reduced in gene content and size as well as a relatively low content of guanine and cytosine. Codon and amino acid preferences that emphasize low guanosine and cytosine usage are globally employed in these genomes, including within regions of microsynteny and within signature sequences of orthologous proteins. The length of orthologous proteins is generally conserved, but not their isoelectric points, consistent with extensive amino acid substitutions to accommodate selection for low GC content. The ‘Ca. Liberibacter asiaticus’ genome apparently has all of the genes required for DNA replication present in Sinorhizobium meliloti except it has only two, rather than three RNaseH genes. The gene set required for DNA repair has only one rather than ten DNA ligases found in Sinorhizobium meliloti, and the DNA PolI of ‘Ca. Liberibacter asiaticus’ lacks domains needed for excision repair. Thus the ability of ‘Ca. Liberibacter asiaticus’ to repair mutations in its genome may be impaired. Both ‘Ca. Liberibacter asiaticus and Bartonella henselae lack enzymes needed for the metabolism of purines and pyrimidines, which must therefore be obtained from the host. The ‘Ca. Liberibacter asiaticus’ genome also has a greatly reduced set of sigma factors used to control transcription, and lacks sigma factors 24, 28 and 38. The ‘Ca. Liberibacter asiaticus’ genome has all of the hallmarks of a reduced genome of a pathogen adapted to an intracellular lifestyle

Plantar povoações no território: (re)construindo a urbanização da capitania do Piauí, 1697-1761

The Piauí province´s urbanization has kept up with since late 17th century a complex process dealt among Portuguese Crown, the regal representatives, the network woven by the Casa da Torre and by the resident population in its countryside. What it was content of Rodelas countryside has begun to build with territorial identity since the foundation of first parish in 1697. Structuring itself discontinuously in time and space, the Piauí had reformed in 1758, year of creation of its autonomous government. And had became urban in 1761 when the king D. José I and marquis of Pombal had framed by the royal letter written in June 19 a territory formed by six towns and one city. Thus, this paper purposes to reconstructing the Piauí province according to agents involved in the urbanization processes. It proposes to deconstructing Crown´s polices by means towns strategically placed in territory aiming at control and "remedy" of routine injustices practiced in Piauí´s hinterlands. The method of presenting this reconstruction draws on interconnection between text (manuscript documents) and image (maps and photography) which in their discourses have represented a Piauí as space of experiences apprehended as much in official dimension as inhabitant´s everyday life.A urbanização da capitania do Piauí acompanhou, desde finais do século XVII, um complexo processo negociado entre a Coroa portuguesa, os representantes régios, a rede clientelar urdida pela Casa da Torre e a população residente em seus sertões. O que antes era conteúdo dos sertões de Rodelas passou a construir-se como identidade territorial a partir da fundação da primeira freguesia, em 1697, dedicada a Nossa Senhora da Vitória. Estruturando-se descontinuamente no tempo e no espaço, o Piauí reforma-se em 1758, ano da autonomização do seu governo. E fez-se urbano em 1761, quando D. José I e o marquês de Pombal equacionaram, por meio da carta régia de 19 de junho, um território formado por seis vilas e uma cidade. Nessa direção, o objetivo deste artigo consiste em reconstruir o processo de formação da capitania do Piauí segundo os agentes envolvidos na urbanização do território. Propõe-se descortinar as políticas da Coroa por meio da oficialização de povoações estrategicamente locadas no território visando o controle e o "remédio" das injustiças rotineiras do Piauí. O método de apresentar essa reconstrução vale-se da interconexão entre texto (documentação manuscrita) e imagem (mapas e fotografias), que em suas entrelinhas representam um Piauí como espaço de experiências sentidas tanto na dimensão oficial quanto no cotidiano dos seus moradores

Global Patterns and Controls of Nutrient Immobilization On Decomposing Cellulose In Riverine Ecosystems

Microbes play a critical role in plant litter decomposition and influence the fate of carbon in rivers and riparian zones. When decomposing low-nutrient plant litter, microbes acquire nitrogen (N) and phosphorus (P) from the environment (i.e., nutrient immobilization), and this process is potentially sensitive to nutrient loading and changing climate. Nonetheless, environmental controls on immobilization are poorly understood because rates are also influenced by plant litter chemistry, which is coupled to the same environmental factors. Here we used a standardized, low-nutrient organic matter substrate (cotton strips) to quantify nutrient immobilization at 100 paired stream and riparian sites representing 11 biomes worldwide. Immobilization rates varied by three orders of magnitude, were greater in rivers than riparian zones, and were strongly correlated to decomposition rates. In rivers, P immobilization rates were controlled by surface water phosphate concentrations, but N immobilization rates were not related to inorganic N. The N:P of immobilized nutrients was tightly constrained to a molar ratio of 10:1 despite wide variation in surface water N:P. Immobilization rates were temperature-dependent in riparian zones but not related to temperature in rivers. However, in rivers nutrient supply ultimately controlled whether microbes could achieve the maximum expected decomposition rate at a given temperature

Minimal information for studies of extracellular vesicles 2018 (MISEV2018):a position statement of the International Society for Extracellular Vesicles and update of the MISEV2014 guidelines

The last decade has seen a sharp increase in the number of scientific publications describing physiological and pathological functions of extracellular vesicles (EVs), a collective term covering various subtypes of cell-released, membranous structures, called exosomes, microvesicles, microparticles, ectosomes, oncosomes, apoptotic bodies, and many other names. However, specific issues arise when working with these entities, whose size and amount often make them difficult to obtain as relatively pure preparations, and to characterize properly. The International Society for Extracellular Vesicles (ISEV) proposed Minimal Information for Studies of Extracellular Vesicles (“MISEV”) guidelines for the field in 2014. We now update these “MISEV2014” guidelines based on evolution of the collective knowledge in the last four years. An important point to consider is that ascribing a specific function to EVs in general, or to subtypes of EVs, requires reporting of specific information beyond mere description of function in a crude, potentially contaminated, and heterogeneous preparation. For example, claims that exosomes are endowed with exquisite and specific activities remain difficult to support experimentally, given our still limited knowledge of their specific molecular machineries of biogenesis and release, as compared with other biophysically similar EVs. The MISEV2018 guidelines include tables and outlines of suggested protocols and steps to follow to document specific EV-associated functional activities. Finally, a checklist is provided with summaries of key points